Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2453
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58370
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:619 original size:27 final size:26
Alignment explanation
Indices: 589--744 Score: 134
Period size: 27 Copynumber: 5.7 Consensus size: 26
579 AAATTGTACA
* *
589 GCACTAAGTGTGCGATTCGATTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* *
616 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
643 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
* *
670 GCACTAAGTGTGCGAATCTAACTATGTA
1 GCACTAAGTGTGCG-AT-TGACTATGTG
* * *
698 GCACTAAGGGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
725 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGA-TTGA
745 GTGAATAGCA
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
27 84 0.79
28 23 0.21
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:711 original size:82 final size:81
Alignment explanation
Indices: 589--744 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
579 AAATTGTACA
* * * * * *
589 GCACTAAGTGTGCGATTCGATTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAATCAACTATGTAGCACTAAGGGTGCGAAATGAATACG-TGGCACTAAGTG
653 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
670 GCACTAAGTGTGCGAATCTAACTATGTAGCACTAAGGGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAATC-AACTATGTAGCACTAAGGGTGCGAAATGAATACGTGGCACTAAGTG
*
735 TGCGAGTTGA
65 TGCGAATTGA
745 GTGAATAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 18 0.29
82 45 0.71
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATCAACTATGTAGCACTAAGGGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:6599 original size:27 final size:27
Alignment explanation
Indices: 6562--6766 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
6552 TAAATTGTAC
*
6562 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6589 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
6616 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
6642 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
6670 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6697 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
6725 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
6752 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6767 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:6623 original size:54 final size:54
Alignment explanation
Indices: 6563--6766 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
6553 AAATTGTACA
* * *
6563 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
6617 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
6671 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
6726 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
6767 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:11017 original size:28 final size:30
Alignment explanation
Indices: 10985--11056 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 30
10975 GTGATCAACA
10985 CAGTATCAGTACAATCT-G-AAGCCCTATT
1 CAGTATCAGTACAATCTGGAAAGCCCTATT
11013 CAGTATCAGTACAATCTGGACCAAAGCCCTATT
1 CAGTATCAGTACAATCTGG---AAAGCCCTATT
11046 CAGTATCAGTA
1 CAGTATCAGTA
11057 TAGTGCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
28 17 0.44
29 1 0.03
33 21 0.54
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (30 bp):
CAGTATCAGTACAATCTGGAAAGCCCTATT
Found at i:11734 original size:19 final size:19
Alignment explanation
Indices: 11699--11738 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11689 CATGTGGGCC
*
11699 CACGAGCCCATTGGGCCCA
1 CACGAGCCCATAGGGCCCA
11718 CACG-GCCCATAGAGGCCCA
1 CACGAGCCCATAG-GGCCCA
11737 CA
1 CA
11739 ATAGCTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.25, C:0.42, G:0.25, T:0.07
Consensus pattern (19 bp):
CACGAGCCCATAGGGCCCA
Found at i:14222 original size:28 final size:28
Alignment explanation
Indices: 14190--14316 Score: 173
Period size: 29 Copynumber: 4.5 Consensus size: 28
14180 TAGTAAGTCT
*
14190 GCACACTTAGTGTTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
*
14218 GCACACTTAGTGCTTACATAATCAAACTC
1 GCACACTTAGTGC-TATATAATCAAACTC
*
14247 GCACACTTAGTGCTATATAATCAAACTT
1 GCACACTTAGTGCTATATAATCAAACTC
** * *
14275 GCACACTTAGTGCTATGCAATTTAAACCC
1 GCACACTTAGTGCTATATAA-TCAAACTC
14304 GCACACTTAGTGC
1 GCACACTTAGTGC
14317 CGAAATCAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
28 43 0.49
29 45 0.51
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:14279 original size:57 final size:57
Alignment explanation
Indices: 14190--14316 Score: 184
Period size: 57 Copynumber: 2.2 Consensus size: 57
14180 TAGTAAGTCT
* *
14190 GCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAACCC
* * * *
14247 GCACACTTAGTGCTATATAATCAAACTTGCACACTTAGTGCTATGCAATTTAAACCC
1 GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAACCC
14304 GCACACTTAGTGC
1 GCACACTTAGTGC
14317 CGAAATCAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 60 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (57 bp):
GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAACCC
Found at i:18186 original size:374 final size:374
Alignment explanation
Indices: 17487--18220 Score: 1396
Period size: 374 Copynumber: 2.0 Consensus size: 374
17477 AGAGTGGGGT
* * *
17487 CTTAACTTGTTGCAGTAACCCAGAAGGTACCTGATACTCTGCCTTAACCTGCTGACACGTTAGGC
1 CTTAACCTGCTGCAGTAACCCAGAAGGTACCTGATACTCCGCCTTAACCTGCTGACACGTTAGGC
17552 ACTTACTCACATAATCTGTAACTTCGCGTTTTAACCCAGGCTACCAATACAATTCACGAAGATCC
66 ACTTACTCACATAATCTGTAACTTCGCGTTTTAACCCAGGCTACCAATACAATTCACGAAGATCC
*
17617 CGGTACAACTTGTTCTCACCAGGATACATGGCATAACGGCTACCATGCGCCTCTCACAGAATAGA
131 CGGTACAACTTGTTCTCACCAGGATACATGGCATAACGGCTACCATGCACCTCTCACAGAATAGA
17682 CTGCCTTAGACTAGAATCATTCGGCATACACACTCTTCCACAGAAACATAACACCCCTTCCCCAT
196 CTGCCTTAGACTAGAATCATTCGGCATACACACTCTTCCACAGAAACATAACACCCCTTCCCCAT
17747 TCAGCCCAAAATCAGAAGTCTCACTTTTTCCCACTTGCTAAAAACGAGGAACCAGCGATTCATCC
261 TCAGCCCAAAATCAGAAGTCTCACTTTTTCCCACTTGCTAAAAACGAGGAACCAGCGATTCATCC
17812 AACAACTGTTTCTCCTTAATTTGATCAGTCCAAGTACCTGATACTCCGC
326 AACAACTGTTTCTCCTTAATTTGATCAGTCCAAGTACCTGATACTCCGC
17861 CTTAACCTGCTGCAGTAACCCAGAAGGTACCTGATACTCCGCCTTAACCTGCTGACACGTTAGGC
1 CTTAACCTGCTGCAGTAACCCAGAAGGTACCTGATACTCCGCCTTAACCTGCTGACACGTTAGGC
17926 ACTTACTCACATAATCTGTAACTTCGCGTTTTAACCCAGGCTACCAATACAATTCACGAAGATCC
66 ACTTACTCACATAATCTGTAACTTCGCGTTTTAACCCAGGCTACCAATACAATTCACGAAGATCC
*
17991 CGGTACAACTTGTTCTCACCAGGATACATGGCATAACGGCTACCATGCACCTCTCGCAGAATAGA
131 CGGTACAACTTGTTCTCACCAGGATACATGGCATAACGGCTACCATGCACCTCTCACAGAATAGA
18056 CTGCCTTAGACTAGAATCATTCGGCATACACACTCTTCCACAGAAACATAACACCCCTTCCCCAT
196 CTGCCTTAGACTAGAATCATTCGGCATACACACTCTTCCACAGAAACATAACACCCCTTCCCCAT
* *
18121 TCAGCCGAAAATCAGAAGTCTCACTTTTTCCCACTTGCTGAAAACGAGGAACCAGCGATTCATCC
261 TCAGCCCAAAATCAGAAGTCTCACTTTTTCCCACTTGCTAAAAACGAGGAACCAGCGATTCATCC
*
18186 AACAACTGTTTCTCTTTAATTTGATCAGTCCAAGT
326 AACAACTGTTTCTCCTTAATTTGATCAGTCCAAGT
18221 CGGTCTCACT
Statistics
Matches: 352, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
374 352 1.00
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (374 bp):
CTTAACCTGCTGCAGTAACCCAGAAGGTACCTGATACTCCGCCTTAACCTGCTGACACGTTAGGC
ACTTACTCACATAATCTGTAACTTCGCGTTTTAACCCAGGCTACCAATACAATTCACGAAGATCC
CGGTACAACTTGTTCTCACCAGGATACATGGCATAACGGCTACCATGCACCTCTCACAGAATAGA
CTGCCTTAGACTAGAATCATTCGGCATACACACTCTTCCACAGAAACATAACACCCCTTCCCCAT
TCAGCCCAAAATCAGAAGTCTCACTTTTTCCCACTTGCTAAAAACGAGGAACCAGCGATTCATCC
AACAACTGTTTCTCCTTAATTTGATCAGTCCAAGTACCTGATACTCCGC
Found at i:22311 original size:28 final size:30
Alignment explanation
Indices: 22279--22354 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 30
22269 GTGATCAACA
*
22279 CAGTATCAGTACAGTCT-G-AATCCCTATT
1 CAGTATCAGTACAGTCTGGAAAGCCCTATT
22307 CAGTATCAGTACAGTCTGGGTCAAAGCCCTATT
1 CAGTATCAGTACAGTCT-GG--AAAGCCCTATT
22340 CAGTATCAGTACAGT
1 CAGTATCAGTACAGT
22355 GCATAATGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 17 0.40
30 1 0.02
33 24 0.57
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (30 bp):
CAGTATCAGTACAGTCTGGAAAGCCCTATT
Found at i:25429 original size:13 final size:13
Alignment explanation
Indices: 25411--25436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25401 TATTGATGTA
25411 TTATGTAAGTTAT
1 TTATGTAAGTTAT
25424 TTATGTAAGTTAT
1 TTATGTAAGTTAT
25437 GTAAGTTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTATGTAAGTTAT
Found at i:28600 original size:16 final size:17
Alignment explanation
Indices: 28581--28618 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28571 AGCTAAATTT
*
28581 AAAATTAT-TAAAATAA
1 AAAATTATAAAAAATAA
*
28597 AAAAATATAAAAAATAA
1 AAAATTATAAAAAATAA
28614 AAAAT
1 AAAAT
28619 AATTTAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTATAAAAAATAA
Found at i:31019 original size:18 final size:18
Alignment explanation
Indices: 30993--31027 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30983 GAAAGGCTGA
*
30993 GAAAGAAAAGGGAATCGG
1 GAAACAAAAGGGAATCGG
31011 GAAACAAAAGGGAATCG
1 GAAACAAAAGGGAATCG
31028 TGGGAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
GAAACAAAAGGGAATCGG
Found at i:33643 original size:24 final size:25
Alignment explanation
Indices: 33616--33667 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
33606 GCCTAGCCTC
33616 TTTTAAT-AACTAGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
* * *
33640 TTTTGATAAACTGGGGCAAAGCGCT
1 TTTTAATAAACTAGGGCAAAGCCCT
33665 TTT
1 TTT
33668 AGCACTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:33727 original size:10 final size:10
Alignment explanation
Indices: 33714--33752 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
33704 ATATGTGAAT
33714 ATATCATGGC
1 ATATCATGGC
33724 ATATCATGTGC
1 ATATCATG-GC
33735 ATATCATGGC
1 ATATCATGGC
33745 ATATCATG
1 ATATCATG
33753 TACAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:33740 original size:21 final size:21
Alignment explanation
Indices: 33714--33753 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
33704 ATATGTGAAT
33714 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
33735 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
33754 ACAAAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:41547 original size:25 final size:25
Alignment explanation
Indices: 41519--41574 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
41509 GGAGGCCTAG
41519 CCTTTTTCAAT-AACTGGGGCAAAGC
1 CCTTTTT-AATAAACTGGGGCAAAGC
*
41544 CCTTTTTGATAAACTGGGGCAAAGC
1 CCTTTTTAATAAACTGGGGCAAAGC
*
41569 GCTTTT
1 CCTTTT
41575 AGCACTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (25 bp):
CCTTTTTAATAAACTGGGGCAAAGC
Found at i:41549 original size:24 final size:24
Alignment explanation
Indices: 41494--41574 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
41484 AGCATAGCTG
**
41494 CTTTATCATATAACTGGAGGCCTAGCC
1 CTTT-TCA-ATAACTGG-GGCAAAGCC
*
41521 TTTTTCAATAACTGGGGCAAAGCC
1 CTTTTCAATAACTGGGGCAAAGCC
** *
41545 CTTTTTGATAAACTGGGGCAAAGCG
1 CTTTTCAAT-AACTGGGGCAAAGCC
41570 CTTTT
1 CTTTT
41575 AGCACTTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 13 0.28
25 27 0.59
26 3 0.07
27 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
CTTTTCAATAACTGGGGCAAAGCC
Found at i:45841 original size:51 final size:49
Alignment explanation
Indices: 45721--45912 Score: 242
Period size: 49 Copynumber: 3.9 Consensus size: 49
45711 ACTATTGTGA
* * *
45721 GGTCACGTGTGTAGTACTAAGTGCAGGC-ACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAATT
* * * *
45769 GGTCACATGTGTAGTACTAAGTGCAAGCTACTATGCATACCCGAAAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAATT
* * *
45818 GTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAATATT
1 G-G-TCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAATT
* * *
45869 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
45913 TAGCTTCAGC
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
48 26 0.21
49 53 0.43
50 2 0.02
51 41 0.34
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAAAATT
Found at i:45899 original size:100 final size:100
Alignment explanation
Indices: 45714--45909 Score: 315
Period size: 100 Copynumber: 1.9 Consensus size: 100
45704 CAAATGAACT
45714 ATTGTGAGGTCACGTGTGTAGTACTAAGTGCAGGCACTACGTGTACCAGATAATTGGTCACATGT
1 ATTGTGA-GTCACGTGTGTAGTACTAAGTGCAGGCACTACGTGTACCAGATAATTGGTCACATGT
45779 GTAGTACTAAGTGCAAGCTACTATGCATACCCGAAA
65 GTAGTACTAAGTGCAAGCTACTATGCATACCCGAAA
*
45815 ATTGTGA-TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-ATATTGGTCGCATG
1 ATTGTGAGTCACGTGTGTAGTACTAAGTGCAGGC-ACTACGTGTACCAGATA-ATTGGTCACATG
* * *
45878 TGTAGTACTAAGTGTAGGCTACTATGCGTACC
64 TGTAGTACTAAGTGCAAGCTACTATGCATACC
45910 AGATAGCTTC
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
99 27 0.30
100 55 0.62
101 7 0.08
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
ATTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCACTACGTGTACCAGATAATTGGTCACATGTG
TAGTACTAAGTGCAAGCTACTATGCATACCCGAAA
Found at i:49253 original size:93 final size:93
Alignment explanation
Indices: 49094--49264 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
49084 GGATGGTTGA
* * *
49094 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
49159 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
49187 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
49252 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
49265 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:49267 original size:46 final size:46
Alignment explanation
Indices: 49098--49269 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
49088 GGTTGAGCAT
* * * *
49098 CCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
49144 CTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
49189 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
49237 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
49270 GGGGCGGCTT
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 2 0.02
46 58 0.56
47 27 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:56722 original size:46 final size:46
Alignment explanation
Indices: 56666--56834 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
56656 TGGTTGAGCA
*
56666 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACG
* * * *
56712 TCTGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCAA--A--CG
* *
56759 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACG
* *
56805 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
56835 TTAGGGGCGG
Statistics
Matches: 101, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
45 10 0.10
46 47 0.47
47 27 0.27
48 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACG
Found at i:56822 original size:93 final size:92
Alignment explanation
Indices: 56663--56832 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 92
56653 GGATGGTTGA
* * *
56663 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
56728 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
* * *
56756 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
56821 TGAGTCGAGTTC
66 TGAGTCGAGTTC
56833 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 7 0.10
93 64 0.90
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Done.